They said the money the Conservatives are contributing is a fraction of what's needed to get the job done.
"The government is allocating less than 0.7 per cent of the amount needed to protect the Great Lakes," the Council of Canadians said in a statement.
Environment Minister Peter Kent paid a visit to the Toronto waterfront Thursday to "highlight" efforts to clean up the Great Lakes and Ottawa's contribution to the cause.
The Conservative government allocated $3.3 million to 46 projects in its 2011-2012 budget for projects on the Canadian side of the lakes.
"The Great Lakes are fundamental to the well-being of millions of Canadians," Kent said.
"Protecting water quality and ecosystem health in the Great Lakes is vital to ensuring that Canadians can continue to depend on this rich ecosystem."
Parts of the Great Lakes have faced serious pollution and degradation issues for years.
Overall, there are 14 "areas of concern" and money under the Great Lakes Sustainability Fund has been provided for 12 of those.
In its response, the council said as much as $500 million would be needed for a "comprehensive plan" to protect the Great Lakes.
"(The) funding announcement is absurdly inadequate," the council said.
According to Environment Canada, three badly degraded areas of 17 originally identified around the Great Lakes have been fully restored in the past two decades.
The fund provides support to remedial projects that focus on contamination cleanup, ways to improve the quality of municipal wastewater, and fish and wildlife habitat rehabilitation.
"This federal announcement of negligible funding for the Great Lakes is all the more farcical, given the government’s plans to remove habitat protection from the Fisheries Act," the council said.
Kent said $530,000 of the $3.3 million would go toward eight projects in the Toronto area.
The money is, in part, being spent on a project to track seasonal movements of fish species such as walleye, pike and carp in the city's harbour to better understand their habitat use.